Surface sediments prokaryotic communities: five years of 16S rRNA amplicon sequencing data from the northernmost part of the Mediterranean Sea

Surface sediments harbour diverse prokaryotic communities that play a key role in biogeochemical cycling and provide valuable insights when compared with water column communities, allowing for a more comprehensive understanding of marine ecosystem functioning. Specifically, this dataset presents prokaryotic community data from 16 surface sediment samples collected seasonally from June 2020 to May 2025 at the C1-LTER station (45°42′2.99″ N, 13°42′36.00″ E; DEIMS.iD https://deims.org/96969205-cfdf-41d8-979f-ff881ea8dc8b ) in the Gulf of Trieste, located in the northeastern Adriatic Sea (Mediterranean Sea). Extracted DNA was sequenced following the 16S Metagenomic Sequencing Library Preparation protocol and run on an Illumina NovaSeq 6000 System. Raw reads were filtered and denoised with DADA2, and taxonomic assignment was performed against the Silva 138.2 99% reference database. The dataset provides useful insights into prokaryotic communities and their seasonal variability over five years. Moreover, a focus on specific taxa is provided, such as Cyanobacteriota and Archaea, highlighting patterns of community variability in the sediment. Finally, it shows seasonal stability and generally consistent taxa distribution over time, as indicated by the high proportion of shared taxa at each taxonomic level. The raw data, deposited in the NCBI Sequence Read Archive (SRA) under BioProject PRJNA1442017, include two sets of sequencing reads obtained from surface sediment samples using the Illumina MiSeq and Illumina NovaSeq 6000 sequencing platforms, for a total of 27 16S rRNA gene sequencing FASTQ files. Overall, these data provide valuable insight into the surface sediment community in the northernmost part of the Mediterranean Sea, contributing to long-term research on sediment prokaryotic communities.